Organic fertilizer significantly mitigates N₂O emissions while increase contributed of comammox Nitrospira in paddy...

Nitrification is the dominant process for nitrous oxide (N₂O) production under aerobic conditions, but the relative contribution of the autotrophic nitrifiers (the ammonia-oxidising archaea (AOA), the ammonia-oxidising bacteria (AOB) and the comammox) to this process is still unclear in some soil types. This is particularly the case in paddy soils under different fertilization regimes. We investigated active nitrifiers and their contribution to nitrification and N₂O production in a range of unfertilized and fertilized paddy soils, using ¹³CO₂-DNA based stable isotope probing (SIP) technique combined with a series of specific nitrification inhibitors, including acetylene (C₂H₂), 3, 4-dimethylpyrazole phosphate (DMPP) and 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO). The soils had a long-term history of fertilizer application, including chemical fertilizer only, a mixture of chemical fertilizers (70 %) and chicken manure (30 %) or a mixture of rice straw and chemical fertilizers. ¹³CO₂-DNA-SIP and Illumina MiSeq sequencing demonstrated that comammox clades A.1 and B were active nitrifiers in all fertilized paddy soils. Inhibitor experiment showed that AOB largely contributed to nitrification activity and N₂O emission in all paddy soils, while comammox contribution was more significant than AOA. Fertilization considerably altered nitrifiers' relative contribution to nitrification activity and N₂O emissions. Applying organic fertilizers significantly decreased the N₂O emissions but increased the contribution of comammox to the process. These findings expand the functional ecological niche of comammox, revealing their nitrification role and N₂O production in other ecosystems than oligotrophic habitats.